Verification of RootPPL on the Bird Trees

Viktor Senderov
01 Apri 2021

What I tested?

trees
[1] "Accipitridae" "BC7"          "P20b"         "TitTyranRest"
num_nodes
[1] 349 179 249 631
depth
[1] 30 14 15 22
  • 10,000 and 100,000 particles
  • Comparison to Birch results

Models and priors

Models:

[1] "clads2-d-λ"    "clads2-d-λμ"   "clads2-d-λμασ" "clads2"       
[5] "crbd-d-λ"      "crbd-d-λμ"     "crbd"          "birch-clads2" 
[9] "birch-crbda"  
  • Survivorship bias correction for CRBD not implemented in RootPPL

Priors:

floating_t kLambda  = 1.0;
floating_t thetaLambda = 1.0;
floating_t epsMin = 0.0;
floating_t epsMax = 1.0;
floating_t kMu  = 1.0;
floating_t thetaMu = 0.5;
floating_t a = 1.0;
floating_t b = 0.2;
  • ρ as needed.

Accipitridae (10,000)

alt text

evaluate_tree(prepare_tree(1))
                       var   R
clads2-d-λ     3.846580000  20
clads2-d-λμ    3.906802895  20
clads2-d-λμασ  1.541363158  20
clads2         0.845051316  20
crbd-d-λ                NA   1
crbd-d-λμ      2.209953684  20
crbd          21.409518684  20
birch-clads2   1.016323218 500
birch-crbda    0.006285234 500
num_nodes[1]
[1] 349
depth[1]
[1] 30

Accipitridae (100,000)

alt text

evaluate_tree(prepare_tree(1))
                      var   R
clads2-d-λ    0.155141818  11
clads2-d-λμ   0.255706667  15
clads2-d-λμασ 0.114798095  15
clads2        0.237563810  15
crbd-d-λ      1.120966667  15
crbd-d-λμ     0.531878095  15
crbd          4.393652381  15
birch-clads2  1.016323218 500
birch-crbda   0.006285234 500
num_nodes[1]
[1] 349
depth[1]
[1] 30

BC7 (10,000)

alt text

evaluate_tree(prepare_tree(2))
                     var   R
clads2-d-λ    3.46137133   4
clads2-d-λμ   1.64821778  20
clads2-d-λμασ 0.65482912  20
clads2        0.14256552  20
crbd-d-λ              NA   1
crbd-d-λμ     0.38469721  20
crbd          0.73701499  20
birch-clads2  0.74300808 500
birch-crbda   0.01485966 500
num_nodes[2]
[1] 179
depth[2]
[1] 14

BC7 (100,000)

alt text

evaluate_tree(prepare_tree(2))
                     var   R
clads2-d-λ    0.61351217  15
clads2-d-λμ   0.23900492  15
clads2-d-λμασ 0.10269270  15
clads2        0.01260710  15
crbd-d-λ      0.97300421  15
crbd-d-λμ     0.04667570  15
crbd          0.07152555  15
birch-clads2  0.74300808 500
birch-crbda   0.01485966 500
num_nodes[2]
[1] 179
depth[2]
[1] 14

P20b (10,000)

alt text

evaluate_tree(prepare_tree(3))
                     var   R
clads2-d-λ    0.37617343   8
clads2-d-λμ   0.52025194  20
clads2-d-λμασ 0.23428645  20
clads2        0.03408383  20
crbd-d-λ              NA   1
crbd-d-λμ     0.34765827  20
crbd          6.95280441  20
birch-clads2  0.28441072 500
birch-crbda   0.01570452 500
num_nodes[3]
[1] 249
depth[3]
[1] 15

P20b (100,000)

alt text

evaluate_tree(prepare_tree(3))
                     var   R
clads2-d-λ    0.10591389  15
clads2-d-λμ   0.06628198  15
clads2-d-λμασ 0.01713978  15
clads2        0.00157300  15
crbd-d-λ      1.83595795  15
crbd-d-λμ     0.04814338  15
crbd          0.36755270  15
birch-clads2  0.28441072 500
birch-crbda   0.01570452 500
num_nodes[3]
[1] 249
depth[3]
[1] 15

TitTyranRest (10,000)

alt text

evaluate_tree(prepare_tree(4))
                       var   R
clads2-d-λ      6.38903864  12
clads2-d-λμ     4.01094211  20
clads2-d-λμασ   3.86897763  20
clads2          0.29798842  20
crbd-d-λ                NA   1
crbd-d-λμ       7.68952079  20
crbd          263.97796211  20
birch-clads2    1.74480633 500
birch-crbda     0.03113397 500
num_nodes[4]
[1] 631
depth[4]
[1] 22

TitTyranRest (100,000)

alt text

evaluate_tree(prepare_tree(4))
                      var   R
clads2-d-λ     1.29836190   7
clads2-d-λμ    0.40825714  15
clads2-d-λμασ  0.14945714  15
clads2         0.02689524  15
crbd-d-λ       2.14847429  15
crbd-d-λμ      1.14157810  15
crbd          13.64886000  15
birch-clads2   1.74480633 500
birch-crbda    0.03113397 500
num_nodes[4]
[1] 631
depth[4]
[1] 22